molstar 4.2.0 → 4.4.0

package/lib/extensions/mvs/components/custom-label/visual.d.ts

@@ -11,24 +11,24 @@ export declare const CustomLabelTextParams: {
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;

package/lib/extensions/mvs/components/formats.d.ts

@@ -13,24 +13,24 @@ import { MVSData } from '../mvs-data';
 declare const Mvs_base: {
     new (data: {
         mvsData: MVSData;
-        sourceUrl?: string | undefined;
+        sourceUrl?: string;
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: SO.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             mvsData: MVSData;
-            sourceUrl?: string | undefined;
+            sourceUrl?: string;
         };
     };
     type: SO.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{
         mvsData: MVSData;
-        sourceUrl?: string | undefined;
+        sourceUrl?: string;
     }, SO.TypeInfo>;
 };
 /** Plugin state object storing `MVSData` */

package/lib/extensions/mvs/helpers/indexing.d.ts

@@ -37,9 +37,9 @@ export declare const Sorting: {
     create<K extends number, V extends number>(keys: K[], valueFunction: (k: K) => V): Sorting<K, V>;
     /** Return a newly allocated array of keys which have value equal to `target`.
      * The returned keys are sorted by their value. */
-    getKeysWithValue<K_1, V_1 extends number>(sorting: Sorting<K_1, V_1>, target: V_1): K_1[];
+    getKeysWithValue<K, V extends number>(sorting: Sorting<K, V>, target: V): K[];
     /** Return a newly allocated array of keys which have value within interval `[min, max]` (inclusive).
      * The returned keys are sorted by their value.
      * Undefined `min` is interpreted as negative infitity, undefined `max` is interpreted as positive infinity. */
-    getKeysWithValueInRange<K_2, V_2 extends number>(sorting: Sorting<K_2, V_2>, min: V_2 | undefined, max: V_2 | undefined): K_2[];
+    getKeysWithValueInRange<K, V extends number>(sorting: Sorting<K, V>, min: V | undefined, max: V | undefined): K[];
 };

package/lib/extensions/mvs/helpers/schemas.d.ts

@@ -56,6 +56,6 @@ declare const FieldsForSchemas: {
     auth_residue_range: ("auth_asym_id" | "beg_auth_seq_id" | "end_auth_seq_id" | "group_id")[];
     atom: ("label_asym_id" | "label_atom_id" | "label_entity_id" | "label_seq_id" | "type_symbol" | "group_id" | "atom_id" | "atom_index")[];
     auth_atom: ("auth_asym_id" | "auth_atom_id" | "auth_seq_id" | "type_symbol" | "pdbx_PDB_ins_code" | "group_id" | "atom_id" | "atom_index")[];
-    all_atomic: ("auth_asym_id" | "auth_atom_id" | "auth_seq_id" | "label_asym_id" | "label_atom_id" | "label_entity_id" | "label_seq_id" | "type_symbol" | "pdbx_PDB_ins_code" | "beg_label_seq_id" | "beg_auth_seq_id" | "end_label_seq_id" | "end_auth_seq_id" | "group_id" | "atom_id" | "atom_index")[];
+    all_atomic: (keyof typeof AllAtomicCifAnnotationSchema)[];
 };
 export {};

package/lib/extensions/mvs/helpers/utils.d.ts

@@ -55,5 +55,5 @@ export declare function decodeColor(colorString: string | undefined): Color | un
 export type HexColor = `#${string}`;
 export declare const HexColor: {
     /** Decide if a string is a valid hexadecimal color string (6-digit or 3-digit, e.g. '#FF1100' or '#f10') */
-    is(str: any): str is `#${string}`;
+    is(str: any): str is HexColor;
 };

package/lib/extensions/mvs/load-helpers.d.ts

@@ -48,7 +48,7 @@ export declare const UpdateTarget: {
     /** Create a new update, with `selector` pointing to the root. */
     create(plugin: PluginContext, replaceExisting: boolean): UpdateTarget;
     /** Add a child node to `target.selector`, return a new `UpdateTarget` pointing to the new child. */
-    apply<A extends StateObject<any, StateObject.Type<any>>, B extends StateObject<any, StateObject.Type<any>>, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget;
+    apply<A extends StateObject, B extends StateObject, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget;
     /** Delete all children of `target.selector`. */
     deleteChildren(target: UpdateTarget): UpdateTarget;
     /** Commit all changes done in the current update. */

package/lib/extensions/mvs/tree/mvs/mvs-builder.d.ts

@@ -85,7 +85,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;
@@ -266,7 +265,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;

package/lib/extensions/rcsb/validation-report/representation.d.ts

@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -80,6 +81,7 @@ export declare const InterUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -130,6 +132,7 @@ export declare const ClashesParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -179,6 +182,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -229,6 +233,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/extensions/sb-ncbr/index.d.ts

@@ -1,3 +1,11 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
 export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';

package/lib/extensions/sb-ncbr/index.js

@@ -1,3 +1,11 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
 export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';

package/lib/extensions/sb-ncbr/tunnels/actions.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateAction } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+export declare const TunnelDownloadServer: {
+    channelsdb: PD.Group<PD.Normalize<unknown>>;
+};
+export declare const DownloadTunnels: StateAction<PluginStateObject.Root, void, PD.Normalize<{
+    source: PD.NamedParams<PD.Normalize<{
+        url: any;
+    }>, "url"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "pdb">;
+}>>;

package/lib/extensions/sb-ncbr/tunnels/actions.js

@@ -0,0 +1,86 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { StateAction } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { TunnelsServerConfig } from './props';
+import { TunnelsFromRawData, SelectTunnel, TunnelShapeProvider } from './representation';
+export const TunnelDownloadServer = {
+    'channelsdb': PD.EmptyGroup({ label: 'ChannelsDB' })
+};
+export const DownloadTunnels = StateAction.build({
+    display: { name: 'Download Tunnels', description: 'Load a tunnels from the provided source and create theirs representations' },
+    from: PluginStateObject.Root,
+    params: (_, plugin) => {
+        return {
+            source: PD.MappedStatic('pdb', {
+                'pdb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' }),
+                }, { isFlat: true, label: 'PDB' }),
+                'alphafolddb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' })
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'url': PD.Group({
+                    url: PD.Url(''),
+                }, { isFlat: true, label: 'URL' })
+            })
+        };
+    }
+})(({ params, state }, plugin) => Task.create('Download Tunnels', async (ctx) => {
+    plugin.behaviors.layout.leftPanelTabName.next('data');
+    const src = params.source;
+    let downloadParams;
+    switch (src.name) {
+        case 'url':
+            downloadParams = [{ url: src.params.url }];
+            break;
+        case 'pdb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/pdb/${src.params.provider.id}` }]
+                : assertUnreachable(src);
+            break;
+        case 'alphafolddb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/alphafill/${src.params.provider.id.toLowerCase()}` }]
+                : assertUnreachable(src);
+            break;
+        default: assertUnreachable(src);
+    }
+    await state.transaction(async () => {
+        var _a;
+        const update = plugin.build();
+        const webgl = (_a = plugin.canvas3dContext) === null || _a === void 0 ? void 0 : _a.webgl;
+        for (const download of downloadParams) {
+            const response = await (await fetch(download.url.toString())).json();
+            const tunnels = [];
+            Object.entries(response.Channels).forEach(([key, values]) => {
+                if (values.length > 0) {
+                    values.forEach((item) => {
+                        tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+                    });
+                }
+            });
+            update
+                .toRoot()
+                .apply(TunnelsFromRawData, { data: tunnels })
+                .apply(SelectTunnel)
+                .apply(TunnelShapeProvider, {
+                webgl,
+            })
+                .apply(StateTransforms.Representation.ShapeRepresentation3D);
+            await update.commit();
+        }
+    }).runInContext(ctx);
+}));

package/lib/extensions/sb-ncbr/tunnels/algorithm.d.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Shape } from '../../../mol-model/shape';
+import { Color } from '../../../mol-util/color';
+import { Tunnel } from './data-model';
+export declare function createSpheresShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    showRadii: boolean;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;
+export declare function createTunnelShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    webgl: WebGLContext | undefined;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;